Transcript Gene7-07

Chapter 7
Using the
genetic code
7.1 Introduction
7.2 Codon-anticodon recognition involves wobbling
7.3 tRNA contains modified bases that influence its
pairing properties
7.4 (There are sporadic alterations of the universal code)
7.5 tRNAs are charged with amino acids by synthetases
7.6 Accuracy depends on proofreading
7.7 Suppressor tRNAs have mutated anticodons that
read new codons
7.8 The accuracy of translation
7.9 tRNA may influence the reading frame
7.1 Introduction
Stop codons are the three
triplets (UAA, UAG,
UGA) which terminate
protein synthesis.
7.1 Introduction
Figure 7.1 All the
triplet codons have
meaning: 61
represent amino
acids, and 3 cause
termination (STOP).
7.1 Introduction
Figure 7.2 The
number of codons
for each amino acid
does not correlate
closely with its
frequency of use in
proteins.
7.2 Codon-anticodon recognition
involves wobbling
Wobble hypothesis accounts for the
ability of a tRNA to recognize more
than one codon by unusual (non-G C,
non-A T) pairing with the third base
of a codon.
7.2 Codon-anticodon recognition involves wobbling
Figure 7.3 Third bases
have the least influence
on codon meanings.
Boxes indicate groups
of codons within which
third-base degeneracy
ensures that the
meaning is the same.
7.2 Codon-anticodon
recognition involves
wobbling
Figure 7.4 Wobble in
base pairing allows G-U
pairs to form between
the third base of the
codon and and the first
base of the anticodon.
7.2 Codon-anticodon recognition involves wobbling
Figure 7.5 Codon-anticodon pairing involves
wobbling at the third position.
7.3 tRNA contains modified bases that
influence its pairing properties
Modification of DNA or RNA
includes all changes made to the
nucleotides after their initial
incorporation into the
polynucleotide chain.
7.3 tRNA contains
modified bases that
influence its pairing
properties
Figure 7.6 All of
the four bases in
tRNA can be
modified.
7.3 tRNA contains
modified bases that
influence its pairing
properties
Figure 7.7
Modification to
inosine allows
pairing with U, C,
and A.
7.3 tRNA contains
modified bases that
influence its pairing
properties
Figure 7.8
Modification to 2thiouridine restricts
pairing to A alone
because only one Hbond can form with G.
7.3 tRNA contains
modified bases that
influence its pairing
properties
Figure 7.7
Modification to
inosine allows
pairing with U,
C, and A.
7.4 There are sporadic
alterations of the
universal code
Figure 7.9 Changes in the
genetic code in mitochondria
can be traced in phylogeny. The
minimum number of
independent changes is
generated by supposing that the
AUA=Met and the AAA=Asn
changes each occurred
independently twice, and that
the earlyAUA=Met change was
reversed in echinoderms.
7.4 There are sporadic
alterations of the
universal code
Figure 7.9 Changes in the
genetic code in mitochondria
can be traced in phylogeny. The
minimum number of
independent changes is
generated by supposing that the
AUA=Met and the AAA=Asn
changes each occurred
independently twice, and that
the earlyAUA=Met change was
reversed in echinoderms.
7.5 tRNAs are charged with amino acids
by synthetases
Cognate tRNAs are those recognized
by a particular aminoacyl-tRNA
synthetase.
Isoaccepting tRNAs represent the
same amino acid.
7.5 tRNAs are
charged with amino
acids by synthetases
Figure 7.10 An
aminoacyl-tRNA
synthetase charges tRNA
with an amino acid.
7.5 tRNAs are
charged with amino
acids by synthetases
Figure 7.11 An aminoacyltRNA synthetase contains
three or four regions with
different functions. (Only
multimeric synthetases
possess an oligomerization
domain.)
7.5 tRNAs are charged with amino acids by synthetases
Figure 7.12 Crystal structures show that class I and class II
aminoacyl-tRNA synthetases bind the opposite faces of their
tRNA substrates. The tRNA is shown in red, and the protein in
blue. Photographs kindly provided by Dino Moras.
7.5 tRNAs are
charged with amino
acids by synthetases
Figure 7.13 A class I
tRNA synthetase
contacts tRNA at the
minor groove of the
acceptor stem and at
the anticodon.
7.5 tRNAs are charged
with amino acids by
synthetases
Figure 7.14 A class II
aminoacyl-tRNA
synthetase contacts tRNA
at the major groove of the
acceptor helix and at the
anticodon loop.
7.6 Accuracy depends on proofreading
Proofreading refers to any mechanism
for correcting errors in protein or
nucleic acid synthesis that involves
scrutiny of individual units after they
have been added to the chain.
7.6 Accuracy depends
on proofreading
Figure 7.15 Recognition of the
correct tRNA by synthetase is
controlled at two steps. First, the
enzyme has a greater affinity for
its cognate tRNA. Second, the
aminoacylation of the incorrect
tRNA is very slow.
7.6 Accuracy depends
on proofreading
Figure 7.16 When a synthetase
binds the incorrect amino acid,
proofreading requires binding
of the cognate tRNA. It may
take place either by a
conformation change that
causes hydrolysis of the
incorrect aminoacyl-adenylate,
or by transfer of the amino acid
to RNA, following by
hydrolysis.
7.6 Accuracy depends on proofreading
Figure 7.17 The accuracy of charging tRNAIle by
its synthetase depends on error control at two stages.
7.7 Suppressor tRNAs have mutated
anticodons that read new codons
Missense mutations change a single codon and so may
cause the replacement of one amino acid by another in a
protein sequence.
Nonsense codon means a termination codon.
Suppressor (extragenic) is usually a gene coding a
mutant tRNA that reads the mutated codon either in the
sense of the original codon or to give an acceptable
substitute for the original meaning.
7.7 Suppressor tRNAs have
mutated anticodons that
read new codons
Figure 7.18 Nonsense mutations can
be suppressed by a tRNA with a
mutant anticodon, which inserts an
amino acid at the mutant codon,
producing a full length protein in
which the original Leu residue has
been replaced by Tyr.
7.7 Suppressor tRNAs have mutated
anticodons that read new codons
Figure 7.19 Nonsense suppressor tRNAs are
generated by mutations in the anticodon.
7.7 Suppressor tRNAs
have mutated anticodons
that read new codons
Figure 7.20 Missense
suppression occurs when the
anticodon of tRNA is mutated
so that it responds to the wrong
codon. The suppression is only
partial because both the wildtype tRNA and the suppressor
tRNA can respond to AGA.
7.7 Suppressor tRNAs have
mutated anticodons that
read new codons
Figure 7.21 Nonsense
suppressors also read
through natural termination
codons, synthesizing
proteins that are longer
than wild-type.
7.8 The accuracy of translation
◆ 控制正确性的直接机制是将由A位点的空间化学来决定密码子－反密码
子的识别地区。核糖体的几何学决定密码子－反密码子的结合以这样的方
式进行：通过蛋白质S12，S4和S5的结构接受氨酰－tRNA使得正确性或强
或弱。（或者通过它们对rRNA结构的影响力）
◆ 正确性是核糖体运动的间接影响。核糖体的速度可以决定tRNA识别的
可能性，从而决定此过程的有效性。这个模型解释了改变链延长的动力学
可以影响链霉素。相关参数是核糖体运动速度随时间的变化决定了是结合
还是分开，如果肽链形成的速度增大，在氨酰-tRNA逃避之前，在键形成
中不正确的氨酰决定tRNA识别的可能性，从而决定此过程的有效性。这个
模型解释了改变链延长的动力学可以影响链霉素。相关参数是核糖体运动
速度随时间的变化决定了是结合还是分开，如果肽链形成的速度增大，在
氨酰－tRNA逃避之前，在键形成中不正确的氨酰tRNA更容易被诱捕。减
慢蛋白质合成的速度将会给修正。
7.8 The accuracy of translation
◆ 控制正确性的直接机制是将由A位点的空间化学来决定密码子－反密码
子的识别地区。核糖体的几何学决定密码子－反密码子的结合以这样的方
式进行：通过蛋白质S12，S4和S5的结构接受氨酰－tRNA使得正确性或强
或弱。（或者通过它们对rRNA结构的影响力）
◆ 正确性是核糖体运动的间接影响。核糖体的速度可以决定tRNA识别的
可能性，从而决定此过程的有效性。这个模型解释了改变链延长的动力学
可以影响链霉素。相关参数是核糖体运动速度随时间的变化决定了是结合
还是分开，如果肽链形成的速度增大，在氨酰-tRNA逃避之前，在键形成
中不正确的氨酰决定tRNA识别的可能性，从而决定此过程的有效性。这个
模型解释了改变链延长的动力学可以影响链霉素。相关参数是核糖体运动
速度随时间的变化决定了是结合还是分开，如果肽链形成的速度增大，在
氨酰－tRNA逃避之前，在键形成中不正确的氨酰tRNA更容易被诱捕。减
慢蛋白质合成的速度将会给修正。
7.9 tRNA may
influence the
reading frame
Figure 7.22 A +1
frameshift is required for
expression of the tyb gene
of the yeast Ty element.
The shift occurs at a 7 base
sequence at which two Leu
codon(s) are followed by a
scarce Arg codon.
7.9 tRNA may
influence the
reading frame
Figure 7.22 A +1
frameshift is required for
expression of the tyb gene
of the yeast Ty element.
The shift occurs at a 7 base
sequence at which two Leu
codon(s) are followed by a
scarce Arg codon.
7.10 Summary
1. The sequence of mRNA read in triplets 5 3
is related by the genetic code to the amino acid
sequence of protein read from N- to C-terminus.
2. Multiple tRNAs may respond to a particular
codon.
3. Each amino acid is recognized by a particular
aminoacyl-tRNA synthetase, which also
recognizes all of the tRNAs coding for that
amino acid.
7.10 Summary
4. Aminoacyl-tRNA synthetases vary widely,
but fall into two general groups according to
the structure of the catalytic domain.
5. Mutations may allow a tRNA to read
different codons; the most common form of
such mutations occurs in the anticodon itself.
6. Frameshifts of the +1 type may be caused
by aberrant tRNAs that read "codons" of 4
bases.